Antibiotic resistance of Klebsiella pneumoniae against the background of the COVID-19 pandemic: experience of the multidisciplinary hospital

• Dmitry V. Tapalski
• Elena V. Karpova
• Olga M. Akulenok
• Vitaly K. Okulich
• Igor I. Generalov
• Natalia Yu. Leskova
• Elena G. Antonova
• Ivan V. Zhiltsov
• Olga V. Osipkina
• Ludmila V. Mozharovskaya
• Oleg Yu. Baranov

Abstract

Frequency of bacterial co-infections among patients with COVID-19 is not high, and over-prescribing of antibiotics may contribute the selection of resistant strains of enterobacteria and gram-negative non-fermenting bacteria.

The aim of the study was to assess the local features of antibiotic resistance of K. pneumoniae and its genetic mechanisms against background of the COVID-19 infection pandemic.

Material and methods. There was selected 37 carbapenem-resistant K. pneumoniae strains isolated in 2016, 2017 and 2020 from hospitalized patients, including 15 strains, isolated from patients with COVID-19 infection. Minimal inhibitory concentrations (MICs) of meropenem and colistin were determined by broth microdilution method. Determination of MICs of eravacycline, ceftazidime/avibactam, meropenem/vaborbactam, imipenem/relebactam was performed using Sensititre diagnostic system on EUMDROXF plates. Susceptibility to 11 combinations of 2 antibiotics was detected by modified method of multiply combination bactericidal testing. For 4 K. pneumoniae strains high-throughput sequencing was performed, followed with the subsequent search for determinants of antibiotic resistance and virulence, assessment of plasmid profiles.

Results. All strains were resistant to meropenem (MIC50 32 mg/l, MIC90 128 mg/l) and produced KPC and OXA-48 carbapenemases. Strains isolated in 2016–2017 were susceptible to colistin (MIC ≤2 mg/l), in 2020 only 26.7% of the strains retained their susceptibility (MIC50 64 mg/l, MIC90 256 mg/l). Susceptibility to combinations of two antibiotics with colistin included reduced from 84.6–100% in 2016–2017 till 26.6–66.7% in 2020. The strains isolated in 2020 retained their susceptibility to ceftazidime/avibactam (MIC ≤1 mg/l). 5 strains resistant to cefiderocol with a MIC 8 mg/l were identified. Strains 2564 and 3125 isolated in 2020 from sputum of patients with COVID-19 infection belonged to different sequence-types (ST12 and ST23) and contained the blaOXA-48 carbapenemase gene, additionally strain 2564 contained the blaKPC-27carbapenemase gene. Resistance to colistin was caused by inactivation of the mgrB genes due to insertion of IS1 and IS5-like transposons.

Conclusion. The performed genetic studies demonstrate a diversity of mechanisms of antibiotic resistance in K. pneumoniae leading to the formation of resistance including to antibiotics that haven’t been used in Belarus till now.

Funding. The study was performed as part of the task «Study of biological and molecular-genetic mechanisms of the formation of resistance to polymyxins in extensively drug resistant gram-negative bacteria and the rationale for combined antibiotic therapy of infections caused by them» SPSR «Fundamental and applied sciences for medicine», 2016–2020.

Conflicts of interest. The authors declare no conflicts of interest.

Contribution. Idea and concept solution – Tapalski D.V.; design – Tapalski D.V., Generalov I.I.; the collection and processing of the material – Akulenok O.M., Okulich V.K., Leskova N.Yu., Antonova E.G.; performing microbiological studies – Karpova E.V., Tapalski D.V., Akulenok O.M.; performing molecular genetic studies – Karpova E.V., Osipkina O.V., Mozharovskaya L.V., Baranov O.Yu.; text design and editing – Tapalski D.V., Generalov I.I., Zhiltsov I.V.

Acknowledgments. The authors are grateful to KhimKhrom ALC, Minsk, for the Sensititer diagnostic systems provided for research.

Keywords:Klebsiella pneumoniae, antibiotic resistance, carbapenemases, colistin, cefiderocol, COVID-19 infection

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